ArticleScientific reports2021
Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Multi-omics integration identifies molecular markers and biological pathways for carcass and meat quality traits in Nellore cattle.Scientific reports · 2025Article
- Multi-omics analysis of flavor differences in pectoral muscles between Wuqin 10 duck and Cherry valley duck.Frontiers in molecular biosciences · 2025Article
- Article
- Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study.Animals : an open access journal from MDPI · 2024Article
- Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies.BMC genomics · 2024Article
- A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa).Scientific data · 2023Article
- Integrated multi-omic data reveal the potential molecular mechanisms of the nutrition and flavor in Liancheng white duck meat.Frontiers in genetics · 2022Article
- Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs.Computational and structural biotechnology journal · 2022Article
- Multi-omics approaches for comprehensive analysis and understanding of the immune response in the miniature pig breed.PloS one · 2022Article
- Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig.BMC genomics · 2021Article
- Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea.Animal cells and systems · 2021Article
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13 authors.
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Abstract
Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop "Nanchukmacdon" a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.
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